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Amy D Willis @amydwillis.bsky.social · Jul 23

Wisdom from @titus.idyll.org on the final day of #STAMPS2025: "There's free as in beer, and there's free as in kittens. #Bioinformatics software is free as in kittens. You have to love and care for them or they... well... yeah."

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Amy D Willis @amydwillis.bsky.social · Jul 22

The question was "...*on the same sequencing run*?"

Amy D Willis @amydwillis.bsky.social · Jul 19

Given that a Poisson regression with log link targets the same parameter as your NB regression, I'd be curious to see the coverage of robust Wald CI's. `rigr` wraps this, so does `raoBust`, so should be easy to add.

(Sorry -- I'm at a workshop today or I'd do it myself)

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Amy D Willis @amydwillis.bsky.social · Jul 19

raoBust doesn't invert score tests @nlaroy.bsky.social, but it does implement (model-misspecification) robust score tests, which are amazing for inference.

Feel free to open a feature request. We'll see what we can do.

github.com/statdivlab/r...

GitHub - statdivlab/raoBust: Generalized Linear Models with robust and non-robust Wald and Rao (score) tests

Generalized Linear Models with robust and non-robust Wald and Rao (score) tests - statdivlab/raoBust

github.com

Amy D Willis @amydwillis.bsky.social · Jul 7

The StatDivLab is getting excited for #STAMPS2025 and working on our lectures for 🤩 Stats Day 😻.

We ran this think-pair-share activity last year and, wow, the ensuing discussion was *very* engaged 😹😅

Reach out if you'd like to attend! Woods Hole, MA, July 14-24 2025. #microbiome #dataanalysis

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Amy D Willis @amydwillis.bsky.social · Jul 1

Agreed that (eg) MAG assembly vs taxonomic estimation makes a huge difference to your answer. Also, please definitely read the Conflict of Interest statement for the shallow shotgun paper and note how much of its claims rely on bioinfomatic subsampling *and not actual shallow sequencing data*

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Reposted by Amy D Willis

Prof. Isabelle Laforest-Lapointe @ilafores.bsky.social · Jun 30

Best workshop you can ever follow

Amy D Willis @amydwillis.bsky.social · Jun 29

We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025.

If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!

Thx for sharing widely! 🤞❤️

Titus Brown @titus.idyll.org · Jun 27

Hi folks, we had a last minute cancellation at MBL STAMPS, the microbiome data analysis course in Woods Hole that runs from July 14th to July 24th. We can provide housing space for a woman. If you or anyone you know is interested, pls drop me an e-mail at [email protected]. Thx!

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Amy D Willis @amydwillis.bsky.social · Jun 30

That's wonderful to hear, Isabelle!! Thanks for sharing, too. Hope to see you there in 2026.

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Amy D Willis @amydwillis.bsky.social · Jun 29

We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025.

If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!

Thx for sharing widely! 🤞❤️

Titus Brown @titus.idyll.org · Jun 27

Hi folks, we had a last minute cancellation at MBL STAMPS, the microbiome data analysis course in Woods Hole that runs from July 14th to July 24th. We can provide housing space for a woman. If you or anyone you know is interested, pls drop me an e-mail at [email protected]. Thx!

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Amy D Willis @amydwillis.bsky.social · May 21

The StatDivLab is *fully* reliant on our NIGMS #MIRA R35 to bring you top-quality statistical methods for microbiome research. #NIH

They are quietly taking MIRAs away from this year's applicants. It's sneaky and scary.

Fight back! Call your reps and tell them to protect science!

Mark Peifer (He, him) @peiferlabunc.bsky.social · May 20

The fantastically successful NIGMS MIRA R35 "expired" on May 17, after the most recent deadline--these removals are the most aggressive attack on American science in the current series of devastating actions 🧪

Gabi Serrato Marks @gserratomarks.bsky.social · May 20

NIH moved up the expiration date for some funding opportunities, effectively *canceling* the next application date without removing it from the standard table. I can't even imagine how many people are still prepping these grants.

👀 List of impacted opportunities:
grants.nih.gov/grants/guide...

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Reposted by Amy D Willis

Ethan White @ethanwhite.weecology.org · May 21

It only takes 2 minutes to help defend our amazing program officers (and many other federal employees) and allow them to keep serving all Americans instead of responding to the whims of a single person

Leslie Rissler @ljrissler.bsky.social · May 21

You have 2 days left to comment (by May 23 at 11:59 pm)!

Go to the link if you don’t want your NSF or NIH program officers who took an oath to the constitution (not a political party) to instead be subject to the whims of a president and fired if they don’t “conform”.

Regulations.gov

www.regulations.gov

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Amy D Willis @amydwillis.bsky.social · May 6

How do I describe data with a lot of zeroes? Sparse.

How do I describe data with a lot of variance? High-variance.

How do I describe data where the totals convey complex information about an unknown quantity I care about? (abundance)

I don't. I just state my assumptions.

GitHub - statdivlab/radEmu

Contribute to statdivlab/radEmu development by creating an account on GitHub.

github.com

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Amy D Willis @amydwillis.bsky.social · May 6

I hope you're all having a better week than me.

😽😽 7/6

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Amy D Willis @amydwillis.bsky.social · May 6

I leave you with the StatDivLab mantra:

1. choose something meaningful to estimate
2. choose a sensible way to estimate it
3. choose tests that control Type 1 error

That's what we will keep doing, even if anonymous reviewers insist on buzzwords.

6/6

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Amy D Willis @amydwillis.bsky.social · May 6

Saying "microbiome data is zero-inflated" leads people to seek out "zero-inflated models." Usually, these are bad methods with bad properties. Stay away. 5/6

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Amy D Willis @amydwillis.bsky.social · May 6

Why does this matter? This sort of thinking leads biologists to trust estimators based on highly-parametrised parametric models that are (1) surely misspecified and (2) have terrible properties under misspecification. 4/6

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Amy D Willis @amydwillis.bsky.social · May 6

Don't get me started on overdispersed, let alone compositional. Microbiome data is none of these, and I'm not new to this field. 3/6

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Amy D Willis @amydwillis.bsky.social · May 6

In fact, if you look at blanks and other control data, you see a lot of incorrect detections. There's better evidence that microbiome data is NON-ZERO inflated than zero-inflated.

2/6

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Amy D Willis @amydwillis.bsky.social · May 6

Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6

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Amy D Willis @amydwillis.bsky.social · Apr 29

How are DOGE & Trump planning to permanently decrease the NIH budget, and how do we fight back? -- by a courageous NIH whistleblower.

Thank you to this brave person for their clear analysis and constructive suggestions. #NIH #DOGE

donmoynihan.substack.com/p/the-nih-bu...

The NIH budget is on a fast track to disaster

An NIH insider explains what Republicans are likely to do next, and what we can do

donmoynihan.substack.com

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Reposted by Amy D Willis

Loïs Maignien, PhD. @loimai.bsky.social · Apr 10

#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025.
A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay!
Apply here until June 1: maignienlab.gitlab.io/ebame

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Amy D Willis @amydwillis.bsky.social · Apr 3

Please take 2 minutes to log that the ACA should be protected and expanded, and that trans healthcare is both the right thing to do and a great investment in Americans and America (or however you want to put it!) 💙💓🤍🤎🖤

emily moonlight @threnody.bsky.social · Mar 23

and if you're like "but trump doesn't listen to courts" or "it'll eventually pass," i have this to say:

every single day a trans person can access the lifesaving, essential healthcare they need is worth fighting for.

it's worth court battles & protests & especially 2 minutes of your time.🧵

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Amy D Willis @amydwillis.bsky.social · Mar 14

absolutely!!!!!!! 🦤❤️🦠

Amy D Willis @amydwillis.bsky.social · Mar 14

We've just released radEmu v2.0.0 🥳🦤😻

`remotes::install_github("statdivlab/radEmu")`

A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!

Release notes: github.com/statdivlab/r...

A screenshot of the release notes for radEmu v2. Text available at https://github.com/statdivlab/radEmu/releases

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Reposted by Amy D Willis

Titus Brown @titus.idyll.org · Mar 4

Hello everyone, the STAMPS course on microbiome data analysis at @mblscience.bsky.social is open until Mar 11, 2025! Join us for a great experience!

Please ALSO check out my co-Director @amydwillis.bsky.social excellent post on how to write a great application: statdivlab.github.io/blog/article...

Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) | Marine Biological Laboratory

The STAMPS course promotes dialogue and the exchange of ideas between experts in environmental and microbiome analysis and offers interdisciplinary bioinformatics and statistical training to practitio...

go.mbl.edu

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